SINGEL NUCLEOTIDE POLYMPRPHISMS OF GROWTH HORMONE GENE IN THREE PANGASIID SPECIES: Pangasionodon hypopthlamamus, Pangaisus Jambal AND Pangasius nasutus
Growth performance in fish is known to be associated with of growth hormone gene. Preliminary study showed that Pangasionodon hypopthalamus and Pangasius Jambal show higher growth performance relative to Pangasius nasutus. It is interesting to know whether difference in growth performance among these species is also reflected in the structure of growth hormone gene. This study was aimed to explore the issue by looking at the profile of single nucleotide polymorphisms (SNP).
Genomic DNA of three pangasiid species were extracted and growth hormone gene were partially amplified in PCR system. DNA sequence of GH gene were obtained through running the sample in Miseq, an Illumina platform of next generation sequencing system. The resulting data were then aligned to both reference sequence, which is sequence of GH gene of Pangasionodon hypopthalamus, available on GeneBank by which SNPs were identified. Alignments were also carried out among species. Following this, deduced amino acid was carried out on exon region to see whether nucleotide substitutions resulted in amino acid changes
Out of 1200 nucleotide sequences obtained from the three species, significant number of SNPs were identified .Alignment between GH sequence P. jambal and P. Hypopthalamus found 61 SNPs, 57 occurred in intron and 4 occurred in exon., while alignment between of P. Nasutus and P. Hypopthalamus found 58 SNPs, being 55 occurred in intron and 3 occurred in exon. Alignment of GH sequence between P. Jambal and P. nasutus found only 25 SNPs, with 23 SNP were found in intron and 3 SNPs were found in exon. Further analyses showed that the nucleotide substitutions occurred in exon are synonymous that does not change the amino acid product. This study might indicate that differences in growth performance among the three pangasiid species may not be associated with differences in the structure of GH gene.